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Liu L, He JH, Wu XQ, Liu JJ, Lv WY, Huang CZ, Liu H, Li CM. Simultaneous detection of multiple microRNAs based on fluorescence resonance energy transfer under a single excitation wavelength. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124788. [PMID: 38986256 DOI: 10.1016/j.saa.2024.124788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
MicroRNAs (miRNAs) play a key role in physiological processes, and their dysregulation is closely related to various human diseases. Simultaneous detection of multiple miRNAs is pivotal to cancer diagnosis at an early stage. However, most multicomponent analyses generally involve multiple excitation wavelengths, which are complicated and often challenging to simultaneously acquire multiple detection signals. In this study, a convenient and sensitive sensor was developed to simultaneously detection of multiple miRNAs under a single excitation wavelength through the fluorescence resonance energy transfer between the carbon dots (CDs)/quantum dots (QDs) and graphene oxide (GO). A hybridization chain reaction (HCR) was triggered by miRNA-141 and miRNA-21, resulting in the high sensitivity with a limit of detection (LOD) of 50 pM (3σ/k) for miRNA-141 and 60 pM (3σ/k) for miRNA-21. This simultaneous assay also showed excellent specificity discrimination against the mismatch. Furthermore, our proposed method successfully detected miRNA-21 and miRNA-141 in human serum samples at a same time, indicating its diagnostic potential in a clinical setting.
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Affiliation(s)
- Lin Liu
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Jia Hui He
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Xiao Qiao Wu
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Jia Jun Liu
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Wen Yi Lv
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Cheng Zhi Huang
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Hui Liu
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
| | - Chun Mei Li
- Key Laboratory of Biomedical Analytics (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China; NMPA Key Laboratory for Quality Monitoring of Narcotic Drugs and Psychotropic Substance, Chongqing 401121, PR China.
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2
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Banerjee A, Pons T, Lequeux N, Dubertret B. Quantum dots-DNA bioconjugates: synthesis to applications. Interface Focus 2016; 6:20160064. [PMID: 27920898 PMCID: PMC5071820 DOI: 10.1098/rsfs.2016.0064] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Semiconductor nanoparticles particularly quantum dots (QDs) are interesting alternatives to organic fluorophores for a range of applications such as biosensing, imaging and therapeutics. Addition of a programmable scaffold such as DNA to QDs further expands the scope and applicability of these hybrid nanomaterials in biology. In this review, the most important stages of preparation of QD-DNA conjugates for specific applications in biology are discussed. Special emphasis is laid on (i) the most successful strategies to disperse QDs in aqueous media, (ii) the range of different conjugation with detailed discussion about specific merits and demerits in each case, and (iii) typical applications of these conjugates in the context of biology.
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Affiliation(s)
| | | | | | - Benoit Dubertret
- Laboratoire de Physique et d'Etude des Matériaux, ESPCI ParisTech, CNRS UMR 8213, Université Pierre et Marie Curie, 10 Rue Vauquelin, 75005 Paris, France
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3
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Banerjee A, Grazon C, Nadal B, Pons T, Krishnan Y, Dubertret B. Fast, Efficient, and Stable Conjugation of Multiple DNA Strands on Colloidal Quantum Dots. Bioconjug Chem 2015; 26:1582-9. [PMID: 25992903 DOI: 10.1021/acs.bioconjchem.5b00221] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel method for covalent conjugation of DNA to polymer coated quantum dots (QDs) is investigated in detail. This method is fast and efficient: up to 12 DNA strands can be covalently conjugated per QD in optimized reaction conditions. The QD-DNA conjugates can be purified using size exclusion chromatography and the QDs retain high quantum yield and excellent stability after DNA coupling. We explored single-stranded and double-stranded DNA coupling, as well as various lengths. We show that the DNA coupling is most efficient for short (15 mer) single-stranded DNA. The DNA coupling has been performed on QDs emitting at four different wavelengths, as well as on gold nanoparticles, suggesting that this technique can be generalized to a wide range of nanoparticles.
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Affiliation(s)
- Anusuya Banerjee
- †Laboratoire de Physique et d'Etude des Matériaux, ESPCI ParisTech, CNRS UMR 8213, Université Pierre et Marie Curie, 10 Rue Vauquelin, 75005 Paris, France
| | | | - Brice Nadal
- ‡Nexdot, 10 rue Vauquelin, 75005 Paris, France
| | - Thomas Pons
- †Laboratoire de Physique et d'Etude des Matériaux, ESPCI ParisTech, CNRS UMR 8213, Université Pierre et Marie Curie, 10 Rue Vauquelin, 75005 Paris, France
| | - Yamuna Krishnan
- §E305A, Physical Sciences Division, Gordon Centre for Integrative Science, 929 57th Street, Chicago, Illinois 60637 United States
| | - Benoit Dubertret
- †Laboratoire de Physique et d'Etude des Matériaux, ESPCI ParisTech, CNRS UMR 8213, Université Pierre et Marie Curie, 10 Rue Vauquelin, 75005 Paris, France
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Vaculovicova M, Adam V, Kizek R. Quantification of nanomaterial bioconjugation based on electrophoretic mobility shift. Electrophoresis 2015; 36:1084-5. [DOI: 10.1002/elps.201500168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/02/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Marketa Vaculovicova
- Department of Chemistry and Biochemistry; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
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5
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Zhang Y, Wang TH. High-resolution quantification by charge-dominant electrophoretic mobility shift of quantum dots. Electrophoresis 2015; 36:1011-5. [DOI: 10.1002/elps.201400577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Yi Zhang
- Institute of Bioengineering and Nanotechnology; Agency of Science; Technology and Research; Singapore
- Department of Biomedical Engineering; Johns Hopkins University; Baltimore MD USA
| | - Tza-Huei Wang
- Departments of Biomedical Engineering and Mechanical Engineering; Sidney Kimmel Comprehensive Cancer Center; Center of Cancer Nanotechnology Excellence; Institute for NanoBioTechnology; Johns Hopkins University; Baltimore MD USA
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6
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Wu TC, Dutta M, Stroscio MA. Agarose gel investigation of quantum dots conjugated with short ssDNA. IEEE Trans Nanobioscience 2014; 12:282-8. [PMID: 25140361 DOI: 10.1109/tnb.2013.2268540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Herein, we investigate the migration distance of quantum-dot-functionalized complexes in electrophoresis. The quantitative study of these moving particles in an electrophoretic environment is modeled using an extended Smoluchowski equation. An extended Smoluchowski equation is proposed to addressed the D(m) to Ln(N) plot slope variation issue present in previous work and agreement between experiment and theory is found. The procedures underlying this work then discusses the potential of using agarose electrophoresis as a mean of monitoring the composition of nano-complexes consisting of quantum dots functionalized with differing numbers of DNA molecules.
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7
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Beh C, Pan D, Lee J, Jiang X, Liu KJ, Mao HQ, Wang TH. Direct interrogation of DNA content distribution in nanoparticles by a novel microfluidics-based single-particle analysis. NANO LETTERS 2014; 14:4729-35. [PMID: 25054542 PMCID: PMC4134141 DOI: 10.1021/nl5018404] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/01/2014] [Indexed: 05/29/2023]
Abstract
Nonviral gene delivery holds great promise not just as a safer alternative to viral vectors in traditional gene therapy applications, but also for regenerative medicine, induction of pluripotency in somatic cells, and RNA interference for gene silencing. Although it continues to be an active area of research, there remain many challenges to the rational design of vectors. Among these, the inability to characterize the composition of nanoparticles and its distribution has made it difficult to probe the mechanism of gene transfection process, since differences in the nanoparticle-mediated transfection exist even when the same vector is used. There is a lack of sensitive methods that allow for full characterization of DNA content in single nanoparticles and its distribution among particles in the same preparation. Here we report a novel spectroscopic approach that is capable of interrogating nanoparticles on a particle-by-particle basis. Using PEI/DNA and PEI-g-PEG/DNA nanoparticles as examples, we have shown that the distribution of DNA content among these nanoparticles was relatively narrow, with the average numbers of DNA of 4.8 and 6.7 per particle, respectively, in PEI/DNA and PEI-g-PEG/DNA nanoparticles. This analysis enables a more accurate description of DNA content in polycation/DNA nanoparticles. It paves the way toward comparative assessments of various types of gene carriers and provides insights into bridging the efficiency gap between viral and nonviral vehicles.
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Affiliation(s)
- Cyrus
W. Beh
- Department
of Biomedical Engineering, Johns Hopkins
School of Medicine, 720
Rutland Avenue, Baltimore, Maryland 21205, United
States
| | - Deng Pan
- Department
of Biomedical Engineering, Johns Hopkins
School of Medicine, 720
Rutland Avenue, Baltimore, Maryland 21205, United
States
| | - Jason Lee
- Department
of Biomedical Engineering, Johns Hopkins
School of Medicine, 720
Rutland Avenue, Baltimore, Maryland 21205, United
States
| | - Xuan Jiang
- Department of Materials Science
and Engineering and Department of Mechanical Engineering, Whiting
School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21212, United States
| | - Kelvin J. Liu
- Department
of Biomedical Engineering, Johns Hopkins
School of Medicine, 720
Rutland Avenue, Baltimore, Maryland 21205, United
States
| | - Hai-Quan Mao
- Department
of Biomedical Engineering, Johns Hopkins
School of Medicine, 720
Rutland Avenue, Baltimore, Maryland 21205, United
States
- Department of Materials Science
and Engineering and Department of Mechanical Engineering, Whiting
School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21212, United States
- Translational
Tissue Engineering Center, Johns Hopkins
School of Medicine, 400
North Broadway, Baltimore, Maryland 21287, United
States
| | - Tza-Huei Wang
- Department
of Biomedical Engineering, Johns Hopkins
School of Medicine, 720
Rutland Avenue, Baltimore, Maryland 21205, United
States
- Department of Materials Science
and Engineering and Department of Mechanical Engineering, Whiting
School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21212, United States
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Abstract
Quantum dots are semiconductor nanocrystals that exhibit exceptional optical and electrical behaviors not found in their bulk counterparts. Following seminal work in the development of water-soluble quantum dots in the late 1990's, researchers have sought to develop interesting and novel ways of exploiting the extraordinary properties of quantum dots for biomedical applications. Since that time, over 10,000 articles have been published related to the use of quantum dots in biomedicine, many of which regard their use in detection and diagnostic bioassays. This review presents a didactic overview of fundamental physical phenomena associated with quantum dots and paradigm examples of how these phenomena can and have been readily exploited for manifold uses in nanobiotechnology with a specific focus on their implementation in in vitro diagnostic assays and biodetection.
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Affiliation(s)
- T R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, NEB 100, 3400 N Charles St., Baltimore, Maryland, USA.
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Qureshi IA, Mehler MF. Developing epigenetic diagnostics and therapeutics for brain disorders. Trends Mol Med 2013; 19:732-41. [PMID: 24145019 DOI: 10.1016/j.molmed.2013.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/30/2013] [Accepted: 09/19/2013] [Indexed: 12/11/2022]
Abstract
Perturbations in epigenetic mechanisms have emerged as cardinal features in the molecular pathology of major classes of brain disorders. We therefore highlight evidence which suggests that specific epigenetic signatures measurable in central - and possibly even in peripheral tissues - have significant value as translatable biomarkers for screening, early diagnosis, and prognostication; developing molecularly targeted medicines; and monitoring disease progression and treatment responses. We also draw attention to existing and novel therapeutic approaches directed at epigenetic factors and mechanisms, including strategies for modulating enzymes that write and erase DNA methylation and histone/chromatin marks; protein-protein interactions responsible for reading epigenetic marks; and non-coding RNA pathways.
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Affiliation(s)
- Irfan A Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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10
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Recent Research Advances of Antibody-conjugated Quantum Dots. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60663-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Ge S, Ge L, Yan M, Song X, Yu J, Liu S. A disposable immunosensor device for point-of-care test of tumor marker based on copper-mediated amplification. Biosens Bioelectron 2013; 43:425-31. [DOI: 10.1016/j.bios.2012.12.047] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/06/2012] [Accepted: 12/20/2012] [Indexed: 12/19/2022]
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12
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Sheu JJC, Choi JH, Guan B, Tsai FJ, Hua CH, Lai MT, Wang TL, Shih IM. Rsf-1, a chromatin remodelling protein, interacts with cyclin E1 and promotes tumour development. J Pathol 2013; 229:559-68. [PMID: 23378270 DOI: 10.1002/path.4147] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 10/22/2012] [Accepted: 11/11/2012] [Indexed: 01/09/2023]
Abstract
Chromosome 11q13.5 containing RSF1 (HBXAP), a gene involved in chromatin remodelling, is amplified in several human cancers including ovarian carcinoma. Our previous studies demonstrated requirement of Rsf-1 for cell survival in cancer cells, which contributed to tumour progression; however, its role in tumourigenesis has not yet been elucidated. In this study, we co-immunoprecipitated proteins with Rsf-1 followed by nanoelectrospray mass spectrometry and identified cyclin E1, besides SNF2H, as one of the major Rsf-1 interacting proteins. Like RSF1, CCNE1 is frequently amplified in ovarian cancer, and both Rsf-1 and cyclin E1 were found co-up-regulated in ovarian cancer tissues. Ectopic expression of Rsf-1 and cyclin E1 in non-tumourigenic TP53(mut) RK3E cells led to an increase in cellular proliferation and tumour formation by activating cyclin E1-associated kinase (CDK2). Tumourigenesis was not detected if either cyclin E1 or Rsf-1 was expressed, or they were expressed in a TP53(wt) background. Domain mapping showed that cyclin E1 interacted with the first 441 amino acids of Rsf-1. Ectopic expression of this truncated domain significantly suppressed G1/S-phase transition, cellular proliferation, and tumour formation of RK3E-p53(R175H) /Rsf-1/cyclin E1 cells. The above findings suggest that Rsf-1 interacts and collaborates with cyclin E1 in neoplastic transformation and TP53 mutations are a prerequisite for tumour-promoting functions of the RSF/cyclin E1 complex.
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Affiliation(s)
- Jim Jinn-Chyuan Sheu
- Department of Pathology, Gynecology and Obstetrics and Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
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Zhang Y, Wang TH. Quantum dot enabled molecular sensing and diagnostics. Am J Cancer Res 2012; 2:631-54. [PMID: 22916072 PMCID: PMC3425091 DOI: 10.7150/thno.4308] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 03/31/2012] [Indexed: 12/23/2022] Open
Abstract
Since its emergence, semiconductor nanoparticles known as quantum dots (QDs) have drawn considerable attention and have quickly extended their applicability to numerous fields within the life sciences. This is largely due to their unique optical properties such as high brightness and narrow emission band as well as other advantages over traditional organic fluorophores. New molecular sensing strategies based on QDs have been developed in pursuit of high sensitivity, high throughput, and multiplexing capabilities. For traditional biological applications, QDs have already begun to replace traditional organic fluorophores to serve as simple fluorescent reporters in immunoassays, microarrays, fluorescent imaging applications, and other assay platforms. In addition, smarter, more advanced QD probes such as quantum dot fluorescence resonance energy transfer (QD-FRET) sensors, quenching sensors, and barcoding systems are paving the way for highly-sensitive genetic and epigenetic detection of diseases, multiplexed identification of infectious pathogens, and tracking of intracellular drug and gene delivery. When combined with microfluidics and confocal fluorescence spectroscopy, the detection limit is further enhanced to single molecule level. Recently, investigations have revealed that QDs participate in series of new phenomena and exhibit interesting non-photoluminescent properties. Some of these new findings are now being incorporated into novel assays for gene copy number variation (CNV) studies and DNA methylation analysis with improved quantification resolution. Herein, we provide a comprehensive review on the latest developments of QD based molecular diagnostic platforms in which QD plays a versatile and essential role.
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